After masking off the parts of the copper-clad board you want to keep, you need to remove the parts you don't want to keep. This is usually done by chemically etching away the copper. There are a lot of different chemical techniques for doing this, each with its own advantages and drawbacks.

None of these chemicals is incredibly dangerous, but they can all be toxic or caustic, and should be treated with care. Eye protection and gloves are a very good idea. Before you start, make sure you know how dangerous each chemical is, and figure out what you will need to do if you spill it or get it on yourself. Washing with plenty of water is usually a good start. For some chemicals you may want to keep a neutralizing agent handy. An MSDS (Materials Safety Data Sheet) for the chemical will give you some basic information.

Contents

Ferric Chloride

This is the most common hobbyist etchant. Ferric chloride, FeCl3, is a brownish substance. It's usually sold in a bottle (dissolved in water, perhaps with a little acid or peroxide) or as a powder (which you have to dissolve in water).

When in solution, ferric chloride is a ferric ion (Fe3+) and a chloride ion (Cl-). The ferric ion reacts with the metallic copper on the circuit board in a redox reaction, producing a ferrous ion (Fe2+) and cuprous or cupric (Cu1+ or Cu2+) copper. The chlorine is just along for the ride. The copper ion, unlike the metallic copper, is soluble, so it leaves the circuit board and goes into solution. The reaction products form a black sludge which settles to the bottom of the etching tank. After etching enough copper, all your Fe3+ is used up and your solution is full of Cu1+, and you need to get more etchant.

Ammonium Persulfate

HydroChloric Acid / Hydrogen Peroxide

Mixing about 1 part HCl (Which can be found at most hardware stores, also known as Muriatic Acid. Ask for concrete cleaner.) into 2 parts Hydrogen peroxide (normally used for cleaning cuts) you can make a fairly powerful etchant. Use gloves and don't breathe the fumes though. This will etch a 3"x5" board in less than 10 minutes. No need to heat it up. I usually like to drill a small hole through the board on a corner and thread a wire or nylon string through to help agitate / remove the board.

When the board is done etching, the etchant will probably look like green kool-aid, from the copper content in it. This stuff is highly corrosive and will burn skin, which is why you should wear gloves. But it is easy to handle, and fairly easy to dispose of. the etchant is easily deactivated with baking soda. Pour enough baking soda into it slowly (to keep it from boiling and overflowing... remember what happens with baking soda/vinegar? ya...) until it is a solid mass, then leave it in the sun to dry. You should contact your local authorities to find out what you should do with it next. Whatever you do, DO NOT dump the stuff down the drain, it will eat through your pipes just like any of the other etchants.

Sodium Persulfate

More environmentally friendly than ferric chloride. Can monitor the etching as initially clear new etchant solution turns blue from the copper ions.

Acid Cupric Chloride

Dead simple etchant made from ordinary, store-bought chemicals (hydrochloric acid and hydrogen peroxide). Has the advantage that it can be regenerated by bubbling oxygen/air through it, or by adding more H2O2. In addition, it doesn't get used up: the etchant bath simply grows with use (kind of like sourdough starter…)
The used etchant also makes a great algecide/pH reducer for your pool (and a whole lot cheaper than that stuff they sell at the pool store).

Mix your HCl and H2O2 1:1 in a non-metalic container, making sure to add the acid slowly to the H2O2. DO NOT ADD THE H2O2 TO THE ACID!!!

After you've masked your board, dip it in the solution and constantly agitate. You should notice a dark green cloud start to come from the board almost immedately which quickly dissapears or turns lighter as it gets further from the surface of the board.

Etching should take about 10min depending on the temperature and how well you agitated the etchant. When all of the copper is gone, dip in water to wash off any stray etchant and stop the reaction.

When done etching, save used etchant in a non-metalic container and mark clearly its contents.

If your etchant has become a dark, murky green color, add a little bit of H2O2 or bubble air/O2 through the solution to regenerate it back to a light, transparent green color.

See links at bottom for more information on the chemistry and some pictures of the process.

Disposal procedures

Flushing used etchant down the drain is a bad idea (and usually illegal) because copper ion is toxic. The usual recommended way to dispose of hobbyist amounts of etchant is to convert it to a solid somehow and dispose of the solid in the trash.